############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL Rbowtie2 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘Rbowtie2’ ... ** using staged installation ** libs ** arch - mkdir -p ../inst (cd adapterremoval && (make CXX="g++ -std=gnu++11" -f Makefile)) make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/adapterremoval' g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c adapterset.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c alignment.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c argparse.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c debug.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c demultiplex.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_enc.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c fastq_io.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c linereader_joined.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_id.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_adapter_rm.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main_demultiplex.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c scheduler.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c strutils.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c threads.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c timer.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c trimmed_reads.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c userconfig.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -c main.cc g++ -std=gnu++11 -O3 -pthread -DNDEBUG -o AdapterRemoval adapterset.o alignment.o argparse.o debug.o demultiplex.o fastq.o fastq_enc.o fastq_io.o linereader.o linereader_joined.o main_adapter_id.o main_adapter_rm.o main_demultiplex.o scheduler.o strutils.o threads.o timer.o trimmed_reads.o userconfig.o main.o cp AdapterRemoval ../../inst/ make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/adapterremoval' (cd bowtie2 && (make CXX="g++" -f Makefile)) make[1]: Entering directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/bowtie2' g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_build.o bt2_build.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from bt2_build.cpp:27: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_build.cpp:27: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_build.cpp:27: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_build.cpp:27: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_build.cpp:27: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ccnt_lut.o ccnt_lut.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ref_read.o ref_read.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o alphabet.o alphabet.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o shmem.o shmem.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o edit.o edit.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_idx.o bt2_idx.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from bt2_idx.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_idx.cpp:25: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_idx.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_io.o bt2_io.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from bt2_io.cpp:25: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_io.cpp:25: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_io.cpp:25: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_io.cpp:25: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_util.o bt2_util.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from bt2_util.cpp:26: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_util.cpp:26: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_util.cpp:26: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_util.cpp:26: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o reference.o reference.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ds.o ds.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o multikey_qsort.o multikey_qsort.cpp In file included from multikey_qsort.h:27, from multikey_qsort.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o limit.o limit.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o random_source.o random_source.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o tinythread.o tinythread.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bowtie_build_main.o bowtie_build_main.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o diff_sample.o diff_sample.cpp In file included from diff_sample.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -o bowtie2-build-s bt2_build.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_build_main.o diff_sample.o g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bt2_search.o bt2_search.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from bt2_search.cpp:33: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from bt2_search.cpp:33: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from bt2_search.cpp:33: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void parseOptions(int, const char**)’: bt2_search.cpp:1458:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1458 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void multiseedSearchWorker(void*)’: bt2_search.cpp:2840:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 2840 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, pp, tid)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:2841:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 2841 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:2867:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 2867 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void multiseedSearchWorker_2p5(void*)’: bt2_search.cpp:3964:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3964 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, pp, tid)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:3965:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3965 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp:3977:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3977 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ bt2_search.cpp: In function ‘void multiseedSearch(Scoring&, const PatternParams&, PatternComposer&, AlnSink&, Ebwt&, Ebwt&, OutFileBuf*)’: bt2_search.cpp:4300:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 4300 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from bt2_search.cpp:33: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:31, from blockwise_sa.h:34, from bt2_idx.h:42, from bt2_search.cpp:33: ds.h: In instantiation of ‘EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]’: ds.h:973:12: required from ‘void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ ds.h:958:3: required from ‘void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ ds.h:569:4: required from ‘void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algobase.h:64, from /usr/include/c++/9/bits/char_traits.h:39, from /usr/include/c++/9/ios:40, from /usr/include/c++/9/ostream:38, from /usr/include/c++/9/iostream:39, from bt2_search.cpp:21: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | struct pair | ^~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o qual.o qual.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o pat.o pat.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o sam.o sam.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o read_qseq.o read_qseq.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed_policy.o aligner_seed_policy.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed.o aligner_seed.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from aligner_seed.cpp:23: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from aligner_seed.cpp:23: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from aligner_seed.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_seed.cpp:23: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from aligner_seed.cpp:23: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_seed2.o aligner_seed2.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_seed2.cpp:22: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from aligner_seed2.h:103, from aligner_seed2.cpp:22: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_seed2.h:103, from aligner_seed2.cpp:22: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_seed2.cpp:22: ds.h: In instantiation of ‘EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]’: ds.h:973:12: required from ‘void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ ds.h:958:3: required from ‘void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ ds.h:569:4: required from ‘void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/utility:70, from aligner_seed2.h:98, from aligner_seed2.cpp:22: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | struct pair | ^~~~ aligner_seed2.cpp: In member function ‘size_t Descent::recalcOutgoing(const Read&, const Scoring&, TAlScore, TAlScore, DescentRedundancyChecker&, EFactory&, const EList&, const EList&, PerReadMetrics&)’: aligner_seed2.cpp:585:14: warning: ‘edge.DescentEdge::nex’ may be used uninitialized in this function [-Wmaybe-uninitialized] 585 | DescentEdge edge; | ^~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_sw.o aligner_sw.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_sw_driver.o aligner_sw_driver.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_sw.h:78, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/bits/locale_conv.h:41, from /usr/include/c++/9/locale:43, from /usr/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_sw.h:78, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_cache.o aligner_cache.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_result.o aligner_result.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o ref_coord.o ref_coord.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o mask.o mask.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o pe.o pe.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aln_sink.o aln_sink.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o dp_framer.o dp_framer.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o scoring.o scoring.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o presets.o presets.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o unique.o unique.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o simple_func.o simple_func.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o random_util.o random_util.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_bt.o aligner_bt.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o sse_util.o sse_util.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse.o aligner_swsse.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o outq.o outq.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_loc_i16.o aligner_swsse_loc_i16.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_ee_i16.o aligner_swsse_ee_i16.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_loc_u8.o aligner_swsse_loc_u8.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_swsse_ee_u8.o aligner_swsse_ee_u8.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o aligner_driver.o aligner_driver.cpp In file included from blockwise_sa.h:34, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’: diff_sample.h:180:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~ diff_sample.h:180:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 180 | if(!diffs[d1]) diffCnt++; diffs[d1] = true; | ^~~~~ diff_sample.h:181:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~ diff_sample.h:181:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 181 | if(!diffs[d2]) diffCnt++; diffs[d2] = true; | ^~~~~ In file included from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: bt2_idx.h: In static member function ‘static std::pair Ebwt::fromStrings(const EList >&, bool, int, int, bool, int32_t, int32_t, int32_t, const string&, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool, bool, bool)’: bt2_idx.h:827:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 827 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: bt2_idx.h:831:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 831 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/include/c++/9/memory:80, from bt2_idx.h:28, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from random_util.h:25, from aligner_seed2.h:101, from aligner_driver.h:78, from aligner_driver.cpp:20: ds.h: In instantiation of ‘EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]’: ds.h:973:12: required from ‘void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ ds.h:958:3: required from ‘void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ ds.h:569:4: required from ‘void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]’ aligner_seed2.h:482:31: required from here ds.h:2456:9: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘struct std::pair’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/utility:70, from aligner_seed2.h:98, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/c++/9/bits/stl_pair.h:208:12: note: ‘struct std::pair’ declared here 208 | struct pair | ^~~~ g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -c -o bowtie_main.o bowtie_main.cpp g++ -O3 -m64 -msse2 -funroll-loops -g3 -Wall -DCOMPILER_OPTIONS="\"-O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY\"" -DPOPCNT_CAPABILITY -fno-strict-aliasing -DBOWTIE2_VERSION="\"2.3.2\"" -DBUILD_HOST="\"Rbowtie2\"" -DBUILD_TIME="\"2017\"" -DCOMPILER_VERSION="\"C++11\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -I third_party -pthread -o bowtie2-align-s bt2_search.o qual.o pat.o sam.o read_qseq.o aligner_seed_policy.o aligner_seed.o aligner_seed2.o aligner_sw.o aligner_sw_driver.o aligner_cache.o aligner_result.o ref_coord.o mask.o pe.o aln_sink.o dp_framer.o scoring.o presets.o unique.o simple_func.o random_util.o aligner_bt.o sse_util.o aligner_swsse.o outq.o aligner_swsse_loc_i16.o aligner_swsse_ee_i16.o aligner_swsse_loc_u8.o aligner_swsse_ee_u8.o aligner_driver.o ccnt_lut.o ref_read.o alphabet.o shmem.o edit.o bt2_idx.o bt2_io.o bt2_util.o reference.o ds.o multikey_qsort.o limit.o random_source.o tinythread.o bowtie_main.o cp bowtie2-align-s ../../inst cp bowtie2-build-s ../../inst make[1]: Leaving directory '/home/biocbuild/bbs-3.13-bioc/meat/Rbowtie2/src/bowtie2' g++ -shared -fPIC -o Rbowtie2.so version_info.cpp installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-Rbowtie2/00new/Rbowtie2/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Rbowtie2)